Figure 9.

Analysis of the destabilization of an ideal β-barrel with purely parallel β-strands (P-barrel) coaxial with a SWNT (3,3) averaged over five independent 10-ns MD runs. Time evolution of: (A) backbone RMSD of all residues; (B) Rg of the side chains located in the inner side of the β-barrel (i.e., N27, I31, and M35) and Rg of the bulky Met³⁵ side chains; (C) fraction of the initial inter-side chain contacts located in the inner side of β-barrel; and (D) the Aβ-Aβ potential energy. For comparison, the same analyses are reported for mixed antiparallel-parallel β-barrel (AP-barrel). We also show in C the top view and side view of the constructed perfect P-barrel with the bulky side chains of M35 in VDW representation.